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I have been experiencing random Manager logouts for some time now. It is quite puzzling, not to mention frustrating. This has been the case for me since 0.9.5+ on a wide array of platforms, PHP/MySQL versions, servers, operating systems, etc.
The manager logouts are so frequent at times that it really is starting to impact productivity and efficiency, especially when re-work is required as a result of lost changes from the unintentional logout.
I made an observation immediately before I was force-logged out this evening... I quickly logged back in and then right before I was logged out again I noticed the same thing that caught my eye on the previous logout:
In the top frame of the manager resides a menu, usually looks something like this:

Right beneath this menu is where you’ll find the "Working..." status indicator, etc.
Now, I noticed right as I was being logged out that the menu had changed! It now looked like this:
Hmmm....very odd. I have been able to replicate this behavior and each time prior to being force logged out, I notice that my menu changes as indicated above.
Looking at the generated HTML is more revealing:
<div id="supplementalNav">
<img src="media/style/MODxLight/images/icons/user_go.png" height="16" width="16">
<a onclick="this.blur();" href="index.php?a=28" target="main">username</a> | <span style="display: none;" id="newMail"><a href="index.php?a=10" title="You got mail" target="main"> <img src="media/style/MODxLight/images/icons/email.png" height="16" width="16"></a></span>
<a onclick="this.blur();" href="index.php?a=10" target="main">Messages <span id="msgCounter"><title>MODx CMF Manager Login</title>(
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<meta name="robots" content="noindex / nofollow">
<style type="text/css"></style>
/* Neutralize styles)</span></a>
| <a href="index.php?a=9" target="main">Help</a>
| <a href="index.php?a=8" target="_top">Logout</a>
| <span title="Website name - MODx 0.9.6 (rev 2767)">0.9.6</span>
</div>
Specifically, this is the HTML that appears out of place:
<span id="msgCounter"><title>MODx CMF Manager Login</title>(
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<meta name="robots" content="noindex / nofollow">
<style type="text/css"></style>
/* Neutralize styles)</span>
Provided you don’t have any messages, normally it would just read:
<span id="msgCounter">(0 / 0)</span>
To be fair, the fact that the AJAX request behind updating the msgCounter container fails doesn’t necessarily indicate that it is the Source of the problem, however it is an initial indicator of things to come.
It appears the request fails as a result of no longer being authenticated. I say this because:
1. <title>MODx CMF Manager Login</title> is contained within the failed msgCounter update
2. Once this glitch is witnessed, any accompanying server-side action performed within the manager is followed by a forced Manager logout.
It would seem that the logout should actually happen earlier, but since authentication cannot be confirmed within the AJAX request, it might not force logout/redirect as intended, resulting in the return of part of the Manager Login page as the AJAX Response?
I’m not sure this puts me any closer to understanding the Source of the mysterious manager logout problem, but at least there is a form of indicator prior to actually being force logged out. I’d be interested if the request(s) behind the msgCounter update/etc are in anyway related to the problem itself.